SNPsnap: a Web-based tool for identification and annotation of matched SNPs

被引：122

作者：

Pers, Tune H. ^{[1
,2
,3
,4
]}

Timshel, Pascal ^{[1
,2
,3
,4
]}

Hirschhorn, Joel N. ^{[1
,2
,3
,5
]}

机构：

[1] Boston Childrens Hosp, Div Endocrinol, Boston, MA 02115 USA

[2] Boston Childrens Hosp, Ctr Basic & Translat Obes Res, Boston, MA 02115 USA

[3] Broad Inst MIT & Harvard, Med & Populat Genet Program, Cambridge, MA 2142 USA

[4] Tech Univ Denmark, Ctr Biol Sequence Anal, Dept Syst Biol, DK-2800 Lyngby, Denmark

[5] Harvard Univ, Sch Med, Dept Genet, Boston, MA 02115 USA

来源：

BIOINFORMATICS | 2015年 / 31卷 / 03期

关键词：

BIOLOGICAL PATHWAYS; ASSOCIATION; LOCI;

D O I：

10.1093/bioinformatics/btu655

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

An important computational step following genome-wide association studies (GWAS) is to assess whether disease or trait-associated single-nucleotide polymorphisms (SNPs) enrich for particular biological annotations. SNP-based enrichment analysis needs to account for biases such as co-localization of GWAS signals to genedense and high linkage disequilibrium (LD) regions, and correlations of gene size, location and function. The SNPsnap Web server enables SNP-based enrichment analysis by providing matched sets of SNPs that can be used to calibrate background expectations. Specifically, SNPsnap efficiently identifies sets of randomly drawn SNPs that are matched to a set of query SNPs based on allele frequency, number of SNPs in LD, distance to nearest gene and gene density.

引用

页码：418 / 420

页数：3

共 15 条

[1]

Hundreds of variants clustered in genomic loci and biological pathways affect human height [J].

Allen, Hana Lango ;

Estrada, Karol ;

Lettre, Guillaume ;

Berndt, Sonja I. ;

Weedon, Michael N. ;

Rivadeneira, Fernando ;

Willer, Cristen J. ;

Jackson, Anne U. ;

Vedantam, Sailaja ;

Raychaudhuri, Soumya ;

Ferreira, Teresa ;

Wood, Andrew R. ;

Weyant, Robert J. ;

Segre, Ayellet V. ;

Speliotes, Elizabeth K. ;

Wheeler, Eleanor ;

Soranzo, Nicole ;

Park, Ju-Hyun ;

Yang, Jian ;

Gudbjartsson, Daniel ;

Heard-Costa, Nancy L. ;

Randall, Joshua C. ;

Qi, Lu ;

Smith, Albert Vernon ;

Maegi, Reedik ;

Pastinen, Tomi ;

Liang, Liming ;

Heid, Iris M. ;

Luan, Jian'an ;

Thorleifsson, Gudmar ;

Winkler, Thomas W. ;

Goddard, Michael E. ;

Lo, Ken Sin ;

Palmer, Cameron ;

Workalemahu, Tsegaselassie ;

Aulchenko, Yurii S. ;

Johansson, Asa ;

Zillikens, M. Carola ;

Feitosa, Mary F. ;

Esko, Tonu ;

Johnson, Toby ;

Ketkar, Shamika ;

Kraft, Peter ;

Mangino, Massimo ;

Prokopenko, Inga ;

Absher, Devin ;

Albrecht, Eva ;

Ernst, Florian ;

Glazer, Nicole L. ;

Hayward, Caroline .

NATURE, 2010, 467 (7317) :832-838

[2]

An integrated map of genetic variation from 1,092 human genomes [J].

Altshuler, David M. ;

Durbin, Richard M. ;

Abecasis, Goncalo R. ;

Bentley, David R. ;

Chakravarti, Aravinda ;

Clark, Andrew G. ;

Donnelly, Peter ;

Eichler, Evan E. ;

Flicek, Paul ;

Gabriel, Stacey B. ;

Gibbs, Richard A. ;

Green, Eric D. ;

Hurles, Matthew E. ;

Knoppers, Bartha M. ;

Korbel, Jan O. ;

Lander, Eric S. ;

Lee, Charles ;

Lehrach, Hans ;

Mardis, Elaine R. ;

Marth, Gabor T. ;

McVean, Gil A. ;

Nickerson, Deborah A. ;

Schmidt, Jeanette P. ;

Sherry, Stephen T. ;

Wang, Jun ;

Wilson, Richard K. ;

Gibbs, Richard A. ;

Dinh, Huyen ;

Kovar, Christie ;

Lee, Sandra ;

Lewis, Lora ;

Muzny, Donna ;

Reid, Jeff ;

Wang, Min ;

Wang, Jun ;

Fang, Xiaodong ;

Guo, Xiaosen ;

Jian, Min ;

Jiang, Hui ;

Jin, Xin ;

Li, Guoqing ;

Li, Jingxiang ;

Li, Yingrui ;

Li, Zhuo ;

Liu, Xiao ;

Lu, Yao ;

Ma, Xuedi ;

Su, Zhe ;

Tai, Shuaishuai ;

Tang, Meifang .

NATURE, 2012, 491 (7422) :56-65

[3]

Ensembl 2014 [J].

Flicek, Paul ;

Amode, M. Ridwan ;

Barrell, Daniel ;

Beal, Kathryn ;

Billis, Konstantinos ;

Brent, Simon ;

Carvalho-Silva, Denise ;

Clapham, Peter ;

Coates, Guy ;

Fitzgerald, Stephen ;

Gil, Laurent ;

Giron, Carlos Garcia ;

Gordon, Leo ;

Hourlier, Thibaut ;

Hunt, Sarah ;

Johnson, Nathan ;

Juettemann, Thomas ;

Kaehaeri, Andreas K. ;

Keenan, Stephen ;

Kulesha, Eugene ;

Martin, Fergal J. ;

Maurel, Thomas ;

McLaren, William M. ;

Murphy, Daniel N. ;

Nag, Rishi ;

Overduin, Bert ;

Pignatelli, Miguel ;

Pritchard, Bethan ;

Pritchard, Emily ;

Riat, Harpreet S. ;

Ruffier, Magali ;

Sheppard, Daniel ;

Taylor, Kieron ;

Thormann, Anja ;

Trevanion, Stephen J. ;

Vullo, Alessandro ;

Wilder, Steven P. ;

Wilson, Mark ;

Zadissa, Amonida ;

Aken, Bronwen L. ;

Birney, Ewan ;

Cunningham, Fiona ;

Harrow, Jennifer ;

Herrero, Javier ;

Hubbard, Tim J. P. ;

Kinsella, Rhoda ;

Muffato, Matthieu ;

Parker, Anne ;

Spudich, Giulietta ;

Yates, Andy .

NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) :D749-D755

[4]

Enrichment of cis-regulatory gene expression SNPs and methylation quantitative trait loci among bipolar disorder susceptibility variants [J].

Gamazon, E. R. ;

Badner, J. A. ;

Cheng, L. ;

Zhang, C. ;

Zhang, D. ;

Cox, N. J. ;

Gershon, E. S. ;

Kelsoe, J. R. ;

Greenwood, T. A. ;

Nievergelt, C. M. ;

Chen, C. ;

McKinney, R. ;

Shilling, P. D. ;

Schork, N. J. ;

Smith, E. N. ;

Bloss, C. S. ;

Nurnberger, J. I. ;

Edenberg, H. J. ;

Foroud, T. ;

Koller, D. L. ;

Scheftner, W. A. ;

Coryell, W. ;

Rice, J. ;

Lawson, W. B. ;

Nwulia, E. A. ;

Hipolito, M. ;

Byerley, W. ;

McMahon, F. J. ;

Schulze, T. G. ;

Berrettini, W. H. ;

Potash, J. B. ;

Zandi, P. P. ;

Mahon, P. B. ;

McInnis, M. G. ;

Zoellner, S. ;

Zhang, P. ;

Craig, D. W. ;

Szelinger, S. ;

Barrett, T. B. ;

Liu, C. .

MOLECULAR PSYCHIATRY, 2013, 18 (03) :340-346

[5]

Chemotherapeutic drug susceptibility associated SNPs are enriched in expression quantitative trait loci [J].

Gamazon, Eric R. ;

Huang, R. Stephanie ;

Cox, Nancy J. ;

Dolan, M. Eileen .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (20) :9287-9292

[6]

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits [J].

Hindorff, Lucia A. ;

Sethupathy, Praveen ;

Junkins, Heather A. ;

Ramos, Erin M. ;

Mehta, Jayashri P. ;

Collins, Francis S. ;

Manolio, Teri A. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (23) :9362-9367

[7]

Genomewide Association Studies - Illuminating Biologic Pathways [J].

Hirschhorn, Joel N. .

NEW ENGLAND JOURNAL OF MEDICINE, 2009, 360 (17) :1699-1701

[8]

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA [J].

Maurano, Matthew T. ;

Humbert, Richard ;

Rynes, Eric ;

Thurman, Robert E. ;

Haugen, Eric ;

Wang, Hao ;

Reynolds, Alex P. ;

Sandstrom, Richard ;

Qu, Hongzhu ;

Brody, Jennifer ;

Shafer, Anthony ;

Neri, Fidencio ;

Lee, Kristen ;

Kutyavin, Tanya ;

Stehling-Sun, Sandra ;

Johnson, Audra K. ;

Canfield, Theresa K. ;

Giste, Erika ;

Diegel, Morgan ;

Bates, Daniel ;

Hansen, R. Scott ;

Neph, Shane ;

Sabo, Peter J. ;

Heimfeld, Shelly ;

Raubitschek, Antony ;

Ziegler, Steven ;

Cotsapas, Chris ;

Sotoodehnia, Nona ;

Glass, Ian ;

Sunyaev, Shamil R. ;

Kaul, Rajinder ;

Stamatoyannopoulos, John A. .

SCIENCE, 2012, 337 (6099) :1190-1195

[9]

Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS [J].

Nicolae, Dan L. ;

Gamazon, Eric ;

Zhang, Wei ;

Duan, Shiwei ;

Dolan, M. Eileen ;

Cox, Nancy J. .

PLOS GENETICS, 2010, 6 (04)

[10]

PLINK: A tool set for whole-genome association and population-based linkage analyses [J].

Purcell, Shaun ;

Neale, Benjamin ;

Todd-Brown, Kathe ;

Thomas, Lori ;

Ferreira, Manuel A. R. ;

Bender, David ;

Maller, Julian ;

Sklar, Pamela ;

de Bakker, Paul I. W. ;

Daly, Mark J. ;

Sham, Pak C. .

AMERICAN JOURNAL OF HUMAN GENETICS, 2007, 81 (03) :559-575

← 1 2 →